Use of a self-compatible diploid potato for mutagenesis and forward genetic studies.

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.

Potato, one of the world's major crop plants, has not been subjected to the types of classical genetic analysis that have been employed in other plants. Being a polyploid outbreeder it has been impossible to generate mutational variation, that in other systems, has played such a critical role in elucidating the mechanisms and processes, which underlie plant developmental and related traits. Genetical studies in potato have been limited to the study of relatively few qualitative traits as well as a large number of continuously varying traits. In this project we will address this issue by using a self-compatible Mexican diploid tuber-bearing species of potato Solanum verrucosum to generate a population of EMS mutagenized plants, with a particular focus on identification of mutations that affect plant development, architecture and tuberization. Pilot experiments conducted at JHI have demonstrated the feasibility of this goal, and a few mutants with drastically altered plant development have been obtained and mapping populations for these are under construction. These mutants will be subjected to further genetic and sequence analysis within this project. To this end we will use a novel method, employing next generation sequencing of mutant and wild type bulks to localize a small number of mutants (up to 5) to a small region of the genome. We will also generate draft genome sequence from the progenitor S. verrucosum genotype (VER54-GW1), which will be mapped to the published DM potato genome assembly, as well as assembled de novo. This will provide a template for mutant mapping and isolation, and in addition, it will provide a valuable set of data for comparative genome analysis in potato, and which will contribute to the 'SOL100' initiative aimed at sequencing 100 Solanaceous plant genomes. One of the existing mutants that has a dwarf phenotype will be tested for its fertility to see whether it is feasible to use this in future mutagenesis studies.

Who will benefit from this research?
The proposal is directly relevant to the BBSRC priority area in Crop Science/Food Security and Living with Environmental Change. The project also builds on BBSRC investment in sequencing the potato genome by generating a draft sequence of a strategically important diploid wild species with unusual biological properties, and to generate a scientific first for potato - a panel of genetic mutants that can be mapped and used to dissect potato biology.
Potato researchers will thus benefit directly. In the longer term, potato breeders and eventually farmers stand to benefit.
The staff employed on the project will benefit by gaining experience in a completely new set of activities. While TGAC staff have extensive experience of carrying out genome assemblies this will be their first potato genome sequencing project, and it will be interesting to see how well the large families of closely related genes and pseudogenes e.g NB-LRR genes assemble. Again while sequence variation analysis is routine, and TGAC have used the SHOREMAP software before, this was on test Arabidopsis data, real life data from a larger genome species will be an interesting test of the technique.

How will they benefit from this research?
TGAC staff will benefit from using new informatics tools and tackling new biological problems. They will have to meet project deadlines, and become more connected with the potato researchers and learn more about the underlying potato biology and genetics.
Potato researchers will benefit by having access to the new genome sequence, plus the mutant resources generated and the methods used to produce and clone them. The increased focus towards 'monogenic trait biology' will also be a benefit to potato scientists who have customarily worked on the analysis of quantitative traits, which has allowed few opportunities for experimental science. For such scientists it is often quite frustrating to find that variation in a complex trait is controlled by several loci of small effect, and analysis ends at the QTL mapping stage! Having the opportunity to work with discontinuous trait variation would open up new scientific vistas that would enable real experimental science to be performed.
Potato researchers, breeders and eventually farmers will be aided by an improved understanding of the potato biology derived from this and future projects. We believe that this project forms an excellent pilot for future potato species and variety resequencing projects which will allow a better understanding of potato biology: plant shape, tuberisation, yield, ability to thrive in a variety of environments and survive pathogens e.g. blight.

The project will provide multi-disciplinary training activities for all staff employed on the project, delivering scientists with a high level of scientific and communication skills. The nature of the work will entail the TGAC researchers acquiring new skills such as using the latest genome assembly tools to combine short and long read technologies, and using bulk segregant methods to clone forward genetic mutants. Because we place great importance on excellent communication between teams, and true understanding of how best to meld genetics and genomics together to solve biological problems, TGAC will host the JHI PDRA for two months, training them in informatics skills to use the genome sequence and identify candidate SNPs from the SHOREMAP technique. This exchange of knowledge and skills is bi-directional, the PDRA will share their deep knowledge of the existing potato genome, genetics and biology to highlight the best genome assembly and how to make it more useful for potato researchers. For example the PDRA will use the genome browser and other tools to highlight areas of the genome that are difficult to assemble or particularly important e.g. the NB-LRR genes and also genome browser tracks that can be used to better highlight features for biologists.